Mercurial > repos > iuc > gemini_load

annotate gemini_macros.xml @ 12:1561834c60bd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:19:19 +0000
parents 269089b363d9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
1 <macros>
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
2 <!-- gemini version to be used -->
6
424f44e3448d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 5
diff changeset
3 <token name="@VERSION@">0.20.1</token>
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
4 <!-- minimal annotation files version required by this version of gemini -->
6
424f44e3448d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 5
diff changeset
5 <token name="@DB_VERSION@">200</token>
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
6
11
269089b363d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
7 <xml name="bio_tools">
269089b363d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
8 <xrefs>
269089b363d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
9 <xref type="bio.tools">gemini</xref>
269089b363d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
10 </xrefs>
269089b363d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
11 </xml>
269089b363d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 7
diff changeset
12
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
13 <xml name="requirements">
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
14 <requirements>
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
15 <requirement type="package" version="@VERSION@">gemini</requirement>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
16 <yield />
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
17 </requirements>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
18 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
19
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
20 <xml name="version_command">
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
21 <version_command>gemini --version</version_command>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
22 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
23
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
24 <xml name="stdio">
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
25 <stdio>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
26 <exit_code range="1:" />
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
27 <exit_code range=":-1" />
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
28 <regex match="Error:" />
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
29 <regex match="Exception:" />
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
30 <yield />
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
31 </stdio>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
32 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
33
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
34 <xml name="citations">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
35 <citations>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
36 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
37 <yield />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
38 </citations>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
39 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
40
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
41 <xml name="annotation_dir">
5
b382ddaf8445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
42 <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
43 <options from_data_table="gemini_versioned_databases">
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
44 <filter type="sort_by" column="0" />
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
45 <filter type="static_value" column="2" value="@DB_VERSION@" />
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
46 </options>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
47 </param>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
48 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
49
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
50 <xml name="infile">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
51 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
52 <options options_filter_attribute="metadata.gemini_version" >
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
53 <filter type="add_value" value="@VERSION@" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
54 </options>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
55 </param>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
56 </xml>
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
57
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
58 <xml name="add_header_column">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
59 <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
60 label="Add a header of column names to the output" />
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
61 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
62
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
63 <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
64 <conditional name="report">
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
65 <param name="report_selector" type="select"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
66 label="Set of columns to include in the variant report table"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
67 help="@HELP@">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
68 <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
69 <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
70 <option value="custom">Custom (report user-specified columns)</option>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
71 </param>
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
72 <when value="full" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
73 <when value="minimal">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
74 <param name="columns" type="hidden" value="@MINIMALSET@" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
75 <param name="extra_cols" type="hidden" value="" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
76 </when>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
77 <when value="custom">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
78 <param name="columns" type="select" display="checkboxes" multiple="true" optional="true"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
79 label="Choose columns to include in the report" help="(--columns)">
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
80 <option value="gene">gene</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
81 <option value="chrom">chrom</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
82 <option value="start">start</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
83 <option value="end">end</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
84 <option value="ref">ref</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
85 <option value="alt">alt</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
86 <option value="impact">impact</option>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
87 <option value="impact_severity">impact_severity</option>
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
88 <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
89 </param>
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
90 <param name="extra_cols" type="text"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
91 label="Additional columns (comma-separated)"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
92 help="Column must be specified by the exact name they have in the GEMINI database, e.g., is_exonic or num_hom_alt, but, for genotype columns, GEMINI wildcard syntax is supported. The order of columns in the list is maintained in the output.">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
93 <expand macro="sanitize_query" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
94 </param>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
95 </when>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
96 </conditional>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
97 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
98
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
99 <xml name="filter" token_argument="--filter">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
100 <param argument="@ARGUMENT@" name="filter" type="text"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
101 label="Additional constraints expressed in SQL syntax"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
102 help="Constraints defined here will become the WHERE clause of the SQL query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'.">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
103 <expand macro="sanitize_query" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
104 </param>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
105 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
106
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
107 <xml name="sanitize_query">
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
108 <sanitizer invalid_char="">
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
109 <valid initial="string.printable">
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
110 <remove value="&apos;" />
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
111 </valid>
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
112 <mapping initial="none">
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
113 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
114 </mapping>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
115 </sanitizer>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
116 </xml>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
117
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
118 <xml name="lenient" token_argument="--lenient" token_truevalue="--lenient" token_help="The exact consequence of this setting depends on the type of inheritance pattern you are looking for (see the tool help below).">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
119 <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
120 label="Include hits with less convincing inheritance patterns"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
121 help= "@HELP@" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
122 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
123
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
124 <xml name="unaffected">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
125 <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
126 label="Report candidates shared by unaffected samples"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
127 help="Activating this option will enable the reporting of variants as candidate causative even if they are shared by unaffected samples in the family tree. The default will only report variants that are unique to affected samples."/>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
128 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
129
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
130 <xml name="min_kindreds" token_label="Minimum number of families with a candidate variant for a gene to be reported" token_help="This is the number of families required to have a variant fitting the inheritance model in the same gene in order for the gene and its variants to be reported. For example, we may only be interested in candidates where at least 4 families have a variant (with a fitting inheritance pattern) in that gene.">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
131 <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
132 label="@LABEL@"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
133 help="@HELP@" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
134 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
135
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
136 <xml name="insert_constraint" token_max_repeat="1">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
137 <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
138 <expand macro="filter" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
139 <yield />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
140 </repeat>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
141 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
142
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
143 <xml name="overwritable_where_default" token_default_where="">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
144 <param name="overwrite_default_filter" type="boolean" checked="false"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
145 label="Overwrite the default constraint of this tool"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
146 help="By default, this tool restricts its analysis to @DEFAULT_WHERE@ and this constraint is applied on top of any constraint expressed above. With this option here selected, your custom constraint, if given, will overwrite the default instead." />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
147 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
148
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
149 <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
150 <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
151 <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
152 label="Restrictions to apply to genotype values" help="">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
153 <expand macro="sanitize_query" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
154 <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
155 </param>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
156 <yield />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
157 </repeat>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
158 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
159
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
160 <xml name="sample_filter">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
161 <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
162 <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
163 label="SQL filter to use to filter the sample table" help="">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
164 <expand macro="sanitize_query" />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
165 <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
166 </param>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
167 <param argument="--in" name="in" type="select"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
168 label="A variant must be in either all, none or any samples passing the sample-query filter"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
169 help="">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
170 <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
171 <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
172 <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
173 <option value="--in only">Return a variant if it is found in any sample passing the sample filter, and in NO sample NOT passing it. (only)</option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
174 <option value="--in only all">Return a variant if is found in ALL samples passing the sample filter, and in NO sample NOT passing it. (only all)</option>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
175 </param>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
176 <expand macro="min_kindreds"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
177 label="Minimum number of families in which a variant must pass the sample filter" help=""/>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
178 <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
179 label="Apply the sample-filter on a family-wise basis" help="If a variant passes the sample filter in at least the minimum number of families specified above it is retained." />
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
180 </repeat>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
181 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
182
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
183 <xml name="region_filter">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
184 <repeat name="regions" title="Region Filter" default="0" min="0"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
185 help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
186 <param name="chrom" type="text" label="Chromosome">
12
1561834c60bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
iuc
parents: 11
diff changeset
187 <validator type="regex" message="A chromosome identifier is required when specifying a region filter. It should start with 'chr'">^chr[0-9a-zA-Z: _.-]+</validator>
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
188 </param>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
189 <param name="start" type="text" label="Region Start">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
190 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
191 </param>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
192 <param name="stop" type="text" label="Region End">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
193 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
194 </param>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
195 </repeat>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
196 </xml>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
197
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
198 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
199 mkdir gemini &&
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
200 ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data &&
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
201 export GEMINI_CONFIG='${annotation_databases.fields.path}' &&
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
202 ]]></token>
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
203
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
204 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
205 #set $sql_expr = str($multiline_sql_expr).strip()
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
206 #if str($sql_expr):
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
207 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
208 #set $sql_expr = $sql_expr.replace('\r', '\n')
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
209 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
210 $cmdln_param '$sql_expr'
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
211 #end if
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
212 </token>
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
213
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
214 <token name="@SET_COLS@">
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
215 #if str($report.report_selector) == 'full':
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
216 #set cols = "*"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
217 #else:
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
218 #if $report.columns and str($report.columns) != '':
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
219 #set $cols = str($report.columns)
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
220 #else
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
221 #set $cols = ''
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
222 #end if
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
223 #if str($report.extra_cols).strip():
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
224 #if $cols:
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
225 #set $cols = $cols + ', ' + str($report.extra_cols)
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
226 #else:
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
227 #set $cols = str($report.extra_cols)
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
228 #end if
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
229 #end if
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
230 #if not $cols:
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
231 #set $cols = "variant_id, gene"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
232 #end if
4
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
233 #end if
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
234 </token>
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
235
264f4601dd1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
236 <token name="@COLUMN_SELECT@">
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
237 @SET_COLS@
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
238 #if $cols != "*"
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
239 --columns '$cols'
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
240 #end if
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
241 </token>
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
242
7
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
243 <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
244 #set $region_elements = []
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
245 #for $r in $regions:
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
246 ## The actual chromosome name needs to be single-quoted
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
247 ## in SQL, so we need to quote the single quotes like the
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
248 ## sanitize_query macro would if the whole was a parameter.
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
249 #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()]
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
250 #if str($r.start).strip():
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
251 #silent $r_elements.append("start >= %d" % int($r.start))
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
252 #end if
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
253 #if str($r.stop).strip():
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
254 #silent $r_elements.append("end <= %d" % int($r.stop))
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
255 #end if
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
256 #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
257 #end for
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
258 ]]>
0e136caab106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
259 </token>
0
7f7fbd50e9dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
260 </macros>